Artificial neural networks were applied to the alcoholism data to reveal nonlinear relationships between intermediate phenotypes, marker identity-by-descent sharing, and the affection status. A variable number of hidden units were considered to achieve a balance between the minimal mean-squared error and over-fitting of the data. The predictability of the affection status based on intermediate phenotype information (event-related potential 300, monoamine oxidase, and gender) was 65% to 75%, and sensitivity/specificity ranged around 50% to 80%. The IBD approach succeeded in identifying the same marker as previous studies, but also found additional peaks.